Novakovic sends Cologne into top ten
Nurnberg shaded possession but failed to find a way past a resolute home defence who were rewarded for their stubbornness when Novakovic struck with only seconds remaining.
Slawomir Peszko also spurned a good opportunity to put Cologne ahead when he fired straight into the arms of Raphael Schafer in the Nurnberg goal.
Nurnberg hit back and had two good chances to take the lead before half-time. Andreas Wolf's curling effort was cleared off the line by the head of Miso Brecko.
Then Jens Hegeler wasted the best chance of the half, failing to beat Cologne goalkeeper Michael Rensing from seven yards after the ball broke to him from a block.
Novakovic then spooned the ball over from close range on 68 minutes as it started to look like he was going to have a frustrating afternoon.
But the Slovenia international took centre stage in the final minutes, firstly by forcing a great save from Schafer with a half-volley before finally breaking the deadlock in injury time.
He made his move into the box at the right time and was picked out by Peszko, this time making no mistake as he converted to give the home side the three points.